Troubleshooting¶
This part of the document will address FAQs, known issues, and work arounds. Please do report to us of issues not listed here, and we will try to keep this document up-to-date.
Conda related¶
Known issues related to conda based installation/execution.
- pandoc compilation fails *
Some users have reported a pandoc error. Pleae try to downgrade to pandoc version 1.19
- Library not loaded (libgfortran.3) *
This issue was encountered in the following scenario:
Conda version: 4.6.2
OSX version: 10.14.4
Error:
Abort trap: 6
dyld: Library not loaded: @rpath/libgfortran.3.dylib
Referenced from: /Users/...../rapid08/lib/R/lib/libRblas.dylib
Reason: image not found
This seems to be an issue with MacOS, and conda usage after recent updates. For some reason these fortran libraries are getting disabled when you activate the conda environment. The workaround is to change the order of PATH variable to access /usr/local/bin, and /usr/bin folders before the Conda environments bin folder.
For instance, the following PATH variable:
/Users/xxx/miniconda2/envs/rapid/bin:/Users/xxx/miniconda2/condabin:/Users/xxx/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Should be changed to:
export PATH=/Users/xxx/miniconda2/condabin:/Users/xxx/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/xxx/miniconda2/envs/rapid/bin
- Library not loaded (libcrypto) *
This issue was encountered in the following scenario:
Conda version: 4.8.4
OSX version: 10.15.6 Beta (19G36e)
Error:
dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib
Referenced from: /Users/siva/opt/anaconda3/envs/rapid10/bin/samtools
Reason: image not found
Abort trap: 6
This seems to be an issue with MacOS, and conda usage after recent updates. For unknown reasons an older version of samtools is getting installed. A workaround is to activate the respective conda environment you created, and update your samtools installation manually to version 1.9. You can use the following command:
conda install samtools==1.9
R - related¶
If there are some errors with R modules, Open R by staying in the conda environment, and update the R modules:
update.packages(ask = FALSE, checkBuilt = TRUE)